A ManifoldCF job cannot be deleted, because it is still considered "in use". This could be due to an old job state that is persisted in one of the temporary tables in HSQLDB (the database component) of ManifoldCF.

Run the following file using the command prompt, and provide the core name (obtained in Step 1) as the parameter for the script:
C:\Program Files (x86)\Ektron\Search2.0\ManifoldCF\core\cleanup-database.bat